The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
The nf-core/scrnaseq pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
You can cite the
nf-core pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.